The second thematic research will involve the CPDR (UCL), and two associated teams of the university of Ghent: the Laboratory of Microbiology (MICRO) and the Research Unit on Knowledge-based Systems (KERMIT).

Prof.  Tom Dedeurwaerdere Coordinator of the thematic sub-network (CPDR - UCL)

Prof.  Paul De Vos (MICRO - UGent)

Prof.  Bernard De Baets (KERMIT - UGent)

Prof.  Peter Dawyndt (MICRO - UGent)

Prof.  Stephan Declerck (MBLA - UCL)

Mr  François Van Hove (MBLA - UCL)

Ms  Christine Frison (CPDR - UCL)

Mr  Bart Van Brabant (MICRO - UGent)

Conference 11-12 June 2008, organised in Ghent by the team of the University of Ghent - Information at "MICROBIAL COMMONS"


This second thematic research examines the contribution of global initiatives for information sharing to collective learning in the field of biodiversity governance. It is developing a comparative analysis of the institutional design of collaborative networks, in order to analyse how reflexive governance can be explicitly part of the strategic working program of international institutions.

Global networks for information sharing may contribute to the realisation of the objectives of the Convention on Biological Diversity (Dawyndt, Dedeurwaerdere and Swings 2006). In particular they may contribute to the preservation of traditional knowledge, to equitable benefit sharing by tracking the flow of the resources and building public domain knowledge for public health and food security, for instance by contributing to knowledge on plant genetic diversity and infectious diseases in the developing countries. However, they may also restrict the ability of the developing nations to access information and resources if the knowledge networks are enclosed by excessive intellectual property standards or electronic fences. Further, they may restrict the flow of information for the international science community if there are no sufficient guarantees that public research or knowledge produced for humanitarian purposes will remain in the public domain.

Most of the learning that occurs in this policy field is focused on the development of technical standards and legal tools. This limited conception of the learning process severely limits the possibility to implement these new standards and tools in a sustainable manner. Indeed, the selection processes of the new technical and legal tools should also take into account the transformation of the norms and beliefs in the different stakeholder communities.

Processes of social learning about conflicting beliefs and norms play a key role in the field of microbiological commons. Some particularly difficult issues that are the subject of ongoing discussion are the protection of traditional knowledge, the regulation of pre-CBD (the Convention of Biological Diversity) resources, and the most appropriate transmission and identification protocols to be used in data sharing.

The expected result is to produce a typology of learning processes in the field of the microbiological commons, to formulate policy proposals for institutional design that is required to increase the reflexive capacities and to develop a prototype model for the sharing of microbiological information – coined the bioportal. This bioportal envisions to be a 'test-case' for the establishment of a sound technological, institutional and legal infrastructure for the ongoing institutional experimentation in the field of the microbiological commons.


Description of the research

WP Biogov 1. Institutional design of global networks for information sharing of microbiological resources (UGent/MICRO-KERMIT, UCL/CPDR-MBLA)

The objective of this first workpackage is to build the framework for institutional analysis that will be used in this thematic research. It considers the different institutions for knowledge sharing that are developed in the field of the microbiological commons that further sustainable use of biodiversity, technology transfer, equitable benefit sharing, protection of traditional knowledge and the building of a robust public domain, with a specific focus on: How do these knowledge networks consider processes of participation and evaluation of the stakeholder communities? How do they allow the building of common knowledge and more coherent preferences on these matters? How are the technical issues framed? Who participates to the selection of the technical and legal tools that govern these networks? How to build trust amongst different normative communities? We mean to point to the insufficiencies of these learning processes and clarify the conditions for enhancing the reflexive capacities that are mobilised in the analysis.

First, because the conditions for organizing open access to data and resources in the life sciences differ widely according to the legal frameworks and the institutional policies in place, we will gather the necessary information on the debate on the organisation of the knowledge commons in the legal and political context with a focus on the EU case and the US case, but discuss other cases such as China and Japan when different from the two prototype cases. We will then, on the basis of this comparative research, systematize the solutions adopted to tackle the collective action problems in different cases of organizing the microbiological science commons.

Second, we will analyze and evaluate successful and non-successful cases of data sharing in the life sciences (Cambia, Human Mutations Databank, GBIF, GenBank, CABRI, etc.), l build a broad set of case studies, identify the most relevant variables for doing institutional analysis, build a typology of the learning processes and analyse their reflexive shortcomings.

Building upon the growing set of case studies in the science commons and upon the growing insights in theory of governance we expect to be able to progressively refine a prototype structure based on:

- A set of technical and legal tools to safeguard the microbiolgocial commons for the public domain, such as public licences, standard contracts, common standards for data transmission, etc.

- A framework for institutional analysis addressing the collective action problems encountered in the knowledge commons and which provides a typology of learning processes

- A set of design principles for enhancing the reflexive capacities of the actors and the institutions

WP Biogov 2. Technical, legal and social analysis of a prototype model - Processes of participation and evaluation : bioportal -emerging social network of active contributors (UGent/MICRO-KERMIT, UCL/CPDR)

The development of a global collaborative network for data sharing that is open for public use should retrieve active participation of a growing network of contributors that can interfere with its management, design decisions and implementation. Only this way the information system can reach the level of completeness that is required to landscape the biological resource commons into dynamic bioportals.

Despite the broadness of the goals set, previous attempts to set up federated information systems that provide unified access to knowledge on micro-organisms have primarily focused on the design of standard exchange formats for biological resource data, without targeting the establishment of more integrative information systems that could place the biological resources within the center point of the different stakeholder communities.

Given the dynamic nature of the microbial knowledge generation process, the magnitude of the scope of integration we intend to achieve and the technical hurdles that still need to be overcome to attain complete interoperability, we do feel it is primordial to tackle the proliferation of information sources by gathering an emerging social network of active contributors around the knowledge network. Communication channels built into the graphical web interface could invite users of the bioportal to report inconsistencies or missing pieces of the microbial information puzzle. We also expect that design and implementation decisions will be influenced by feedback received from users. In order to streamline bi-directional communication among a growing community of users and collaborators, we will disseminate a regular newsletter, open an electronic forum for users to comment on design or implementation decisions, and actively experiment with additional communication channels.

- By engaging seemingly unrelated disciplines, traditional gaps in terminology, approach and methodology might be gradually eliminated.

- With roadblocks to integrative information systems and potential collaboration removed, a true meeting of minds can take place: one that broadens the scope of investigation into biodiversity problems, yields fresh and possibly unexpected insights, and may even give birth to new hybrid disciplines that are more analytically sophisticated.

WP Biogov 3. Technical, legal and social analysis of a prototype model -Technical structure (UGent/MICRO-KERMIT)

In migrating the bioportal from a working prototype to a fully fledged implementation, four technical barriers require further attention: i) synchronisation between the bioportal and an emerging network of BRCs, ii) developing group decision-making models to expand the scope of automated integration, iii) monitoring quality of data provided by the individual BRCs, and iii) supporting interoperability between the global network of BRCs and downstream information on microbial resources disseminated by third-party information providers.

Flexible and scalable integration is accomplished by implementing a ‘knuckles-and-nodes' design to manage the top-level architecture of the bioportal. This divide-and-conquer strategy is in itself an application of the semantic web approach for ‘incremental machine learning'. As an emerging strategy to control machine interpretation of large amounts of data it bundles integrative technologies such as globally unique identifiers (GUIDs), ontologies, web services and workflow management systems. A key issue in the philosophy of the bioportal is its compilation of the BRC knuckle, a carefully managed and curated service that thoroughly understands the heterogeneity of information provided by the individual BRCs. Synchronization with the individual BRCs and monitoring the quality of their provided information are performed inside the BRC knuckle. A major contribution of the BRC knuckle is that it completely hides the internal complexity of a global network of autonomous BRCs to the outside world, giving it the transparency that is necessary for seamless integration with downstream information on microbial resources disseminated by third-party information providers. To demonstrate its full integrative power with these third-party information providers, the bioportal will integrate the BRC knuckle with the public sequence databases (sequence knuckle), scientific publication repositories (publication knuckle) and established microbial taxonomies (taxonomy knuckle).

- The bioportal envisions to overcome some of the problems related to the integration of basic information on microbial resources as disseminated by hundreds of BRCs worldwide with the dynamically growing amount of downstream information that is generated on these organisms.

- Once the bioportal comes to full support of a rich interface based on underlying semantic web technologies, third-party information providers will be able to independently set up cross-references through the bioportal with a transparent network of BRCs.

- Such a dynamically expanding cross-reference model based on a genuine divide-and-conquer strategy truly has the potential to establish wider dissemination of all sorts of knowledge on microbial resources through enhanced discoverability of relevant information and through greater use of metadata for targeting the BRC assets more precisely to different audiences whom it might not otherwise reach.

WP Biogov 4. Testing the prototype model - Application of technology platform and institutional infrastructure of the bioportal for a specific research project (MBLA/UCL)

Knowledge about micro-organisms is constantly increasing with improved technologies. The translation of this accumulated knowledge into benefits for all and not just for experts is crucial. It requires i) accessibility to the information through various portals, ii) integration of different data into comprehensive systems and iii) regulation to data accession to avoid conflicts between intellectual properties rights and the need for accessible shared databases. These aspects will be challenged by the bioportal and implemented through a specific pilot project at MBLA/UCL .

The integration of many types of data (genetic, ecological, biological, chemical, …) into data repositories is technically demanding as these overwhelming numbers of data require complex processing methods and high degrees of data fusion for knowledge generation. It requires translating information into comprehensive systems that integrate traditional data (e.g. morphology), genotypic data (e.g. DNA sequences), novel phenotypic data (e.g. spectroscopy) and other types of information. The access to these commons has to take into consideration the often contradicting interests of commercial entities with non-profit organizations, which might generate conflicts between intellectual properties rights and the need for accessible shared databases.

BRCs all over the world store over one million of microbes in more than 500 collections. BCCM/MUCL represents the fourth world largest collection of filamentous fungi, yeast and arbuscular mycorrhizal fungi storing over 30000 organisms that are diversely described with morphological, genetic, physiological, ecological, and other data . The integration of this proliferation of information into easy-to-use, multi-access, regulated bioportals will be assayed on specific sub-collections of organisms at the MBLA/UCL . The steps will involve i) a diagnostic to address current problems and potentials of sharing information as part of a broad data access to diverse forms of information on microbial commons, ii) the selection of a pilot project on a well-defined subgroup of organisms (filamentous fungi, yeast or arbuscular mycorrhizal fungi) stored at the MBLA/UCL and for which polyphasic data are available, to test the reliability of the bioportal, and iii) a demonstration of the software developed by the implementation of the pilot project.

Information sharing and data management on micro-organisms is still in its infancy.

- The improvement of technologies that generates polyphasic data is receiving increasing interest and will yield an overwhelming number of information that should be challenged through information and communication technologies. Ideally, information systems (such as the bioportal) should be able to create increasingly realistic models of nature, as more and more diverse and complex information will be stored into them.

- This will help facing scientific challenges but also biotechnological challenges (e.g. what is the best organism for a peculiar application). Multi-portal access to information, integrative data storage into comprehensive systems and data regulation access will pave the way to the improved use of polyphasic data and to the cohesive dissemination of knowledge relative to microbial resources. This is a major challenge of BRCs as the MBLA/UCL.



Prof. Jacques Lenoble

Director - Coordinator

Université catholique de Louvain

Centre de Philosophie du Droit [ CPDR]







  • 26-28-29 April 2011 : "Philosophie du droit et enjeux de la gouvernance" by Prof. G.A. Legault (Sherbrooke University) - Louvain-La-Neuve

  • [Programme - Presentations]



Anne Liesse

Administrative Research Coordinator

Université catholique de Louvain

Centre de Philosophie du Droit [ CPDR ]

Place Montesquieu 2

B - 1348 Louvain-la-Neuve